In article <32471408.34A at cs.dal.ca>, Dave Edgell <dedgell at cs.dal.ca>
(Andrew J. Roger) wrote:
>First of all, what Kingdom is Woese losing?
Archaea.
>If you are referring to
>Eukaryota, he placed it at the level of domain while Cavalier-Smith placed
>it at the level of Empire. But taxonomy aside, Eukaryota is not Woese's
>kingdom/domain to lose anyway. The distinctness of eukaryotes has been known
>for many years. Thoughts about this crystallized in the 60's--
>Stanier and Van Neil were the first to put these thoughts in the context
>we normally think of them-- emphasizing the huge gulf in cell structure
>between prokaryotes and eukaryotes.
I don't think that anyone is arguing that eukaryotes should be anything
but a distinct phylogenetic group. The discussion concerns whether the
archaebacteria deserve to be a separate "domain" and whether they are
more closely related to eukaryotes than to eubacteria. One possibility
is that the two earliest branches of the tree of life gave rise to
prokaryotes on the one hand and eukaryotes on the other.
>Margulis reawakened everyone to endosymbiosis (which had been
>more or less out of style for 30-40 years in the West) and everyone
>now pretty much accepts an endosymbiotic origin for mitochondria and plastids.
>So we already know that most eukaryotes are chimaeras in this sense.
>That this had something to do with the origin of eukaryotes per se is much
>less clear. There is no evidence that flagella are of endosymbiotic
>origin. Moreover, there are a few eukaryotic groups which lack organelles
>of symbiotic origin. So it is possible that the eukaryotic condition
>(having nucleus, endomembranes and cytoskeleton etc.) arose prior to any
>endosymbiosis....
I don't think that this is relevant. No one contests the fact that
mitochondria and plastids arose from prokaryotic ancestors.
>As for Gupta. He has shown that there are many trees which look like:
>(Archaebacteria,Gm+ve)(Eukaryotes,G,-ves) IF (and this is the big catch)
>you sample few enough taxa from each group.
There are other ways of interpreting the data. For example, I think that
the HSP70 tree is ((archaebacteria, Gm+ve) Gm-ve) eukaryotes). Some of
the other gene dendrograms mentioned by Gupta and Golding may also look
like this and not the way that they present them.
>All 7 of Gupta and Goldings proteins showing the above topology are
>complicated by one or several of the following problems:
>-multiple phylogenetically distinct homologs in single organisms
>(GS, proC, GDH)
>-group polyphyly (all)
>-probable cases of lateral transfer (GS, GDH, aat, hsp70)
>-comparisons of NON-HOMOLOGOUS proteins (ferredoxins of 2FE-2S and
4Fe-4S types)
You raise a number of interesting problems but don't forget that many of
them also apply to those genes that seem to support Woese's Three Domain
Hypothesis. We should be skeptical of *all* current hypotheses concerning
the tree of life.
Besides, I don't agree that "all 7 of Gupta and Goldings proteins" show
the topology that you mention.
>If you look at this data close enough (and believe me I have), you are
>left with a distinct feeling that there is a lot of lateral transfer and/or
>paralogy at the deepest phylogenetic levels and that none of the 7 proteins
>are clean gene phylogenies which are likely to reflect organismal
>relationships only.
Do you believe that there are "clean gene phylogenies" that unequivocally
support the Three Domain Hypothesis? Which ones?
>Until the confusing influences of paralogy and transfer are understood
>in these datasets we must be very careful interpreting this evidence
>solely in terms of organismal relationships.
Agreed. This applies to *all* proposed hypotheses.
>So...has Woese lost a kingdom?
Yes. Archaea. The evidence supporting this distinct monophyletic domain
is much weaker than Woese would have us believe. You have already pointed
out some of the problems.
>- there is no clear evidence for eukaryotes being chimaeric beyond
>organellar endosymbiosis
You are making the assumption that the archaebacteria and eukaryotes are
related and rejecting the data that suggests otherwise. It is just as
logically consistant to conclude that the conflicting phylogenies are
correct and that archaebacteria do not cluster with eukaryotes. We need
more data and more careful attention to what the data actually says.
As far as I am concerned the entire question is up in the air. There is
no good reason to assume that Woese is correct at this time.
Larry Moran